In edit mode, there is an origin located off the side of it's face. It ends up clumping everything together when subdivided. How do I fix this please?
This is most likely because of the face at the bottom that is not visible to us. Subdivision Surface modifier divides concave face like that - this is normal. If you wish to avoid that you should divide the bottom face so it consists of a few convex faces instead of one concave face.